EPA Administrator Lisa Jackson didn’t even have the keys to her office when the Obama administration started its ambitious revamp of her agency.

Immediately after swearing Jackson into her new post, President Barack Obama ordered her to review a Bush administration ruling that prohibited California and 15 other states from setting tougher auto emissions standards. Then, he ordered the Transportation Department to enforce tougher fuel efficiency standards by 2011.

The administration’s message was clear: A new, greener day has dawned at the Environmental Protection Agency.

EPA was one of the most demoralized agencies in the federal government under President George W. Bush. The career staff — which supports stricter environmental regulation — bristled under political appointees who blocked agency initiatives. Their frustration was shared by many in the environmental community, including Jackson. As head of New Jersey’s Department of Environmental Protection, she joked that in the Bush administration, EPA stood for the “Emissions Permissions Agency.”

Now, Jackson is quickly moving forward on a host of once-stalled proposals. In the first 100 days, EPA has taken initial steps to impose stricter controls on coal plants, mercury produced by power plants and greenhouse gas emissions.

“Lisa Jackson took over a listing battleship, and she has righted it and turned it around,” said Dan Weiss, director of climate strategy at the left-leaning Center for American Progress. “Probably no federal agency will have undergone such a profound change than EPA under Obama.”

Gold Medal Performance

The EPA took a major step toward capping greenhouse gas emissions when it issued a much-anticipated finding this month that global warming is a danger to human health and welfare. The finding will have a huge economic impact on coal plants, transportation and manufacturing. It also increases the pressure for Congress to pass climate change legislation before international climate talks in Copenhagen in December. If lawmakers fail to act, the ruling could force EPA to impose strict new regulations.

Worst Train Wreck

One early letdown came when Jon Cannon, a former top EPA lawyer, withdrew his nomination for deputy administrator. The move came after vetters began scrutinizing a now-defunct nonprofit group where Cannon once served on the board of directors that was faulted for mishandling federal grant money.

Sea Change

In a memo to EPA employees, Jackson laid out the administration’s guiding principles: science, rule of law and transparency. And EPA is backed by an administration that counts global warming as one of its top priorities. “There is no example, much less a recent example, of this amount of high-level policy attention being devoted to global warming, clean energy and green jobs,” says John Walke, clean air director for the Natural Resources Defense Council. “We’re in uncharted territory.”

Elephant in the Room

Observers say it will take a long time to undo some of the Bush administration actions that the new administration would like to reverse — such as the easing of prohibitions against dumping mine waste near streams and years of little action on regulating greenhouse gases.

Biggest Food Fight

EPA could soon find itself in a turf war with the Department of Transportation, since both are authorized to address auto emissions. Currently, EPA is reviewing whether to grant states a legal waiver to lower passenger car emissions by 30 percent, while DOT recently revised the federal corporate average fuel economy, or CAFE, standards. Depending on what EPA decides, the two agencies could release conflicting emissions standards: one for states that get the waiver and another that would be applied nationwide.